I've been trying without success to phase the variants of about 30 samples in a 5Mb non-recombining region. I have a phased genome assembly of the region but so far I have not been successful in using that to inform the phasing of the samples which have been sequenced to high coverage with short reads. Non-reference panel phasing using Beagle 5.2 and Shapeit4 have produced haplotypes that are composed of many small phased blocks which switch phase between them, far to many to manually correct.

I have created a "reference panel" of SNPs of known phase for the region and want to use it to guide the rest of the phasing of the non-"reference panel" SNPs but every method I have found only uses the intersection of the reference panel and the samples for analysis. Is there some technique that I can use to phase the genotypes in the samples? I believe this is a tractable problem since recombination is suppressed in this region so haplotype blocks should be large and contiguous.